I don't think he killed anyone in Season 1
I looked up summaries of the first few episodes, where I though he'd killed people. Turns out it's more like the villains died due to other factors. The first Weather Wizard in the pilot was shot by Joe. The villain in episode 2 basically committed suicide while Barry was trying to save him. I thought the Mist in episode 3 had been killed by the Flash, but apparently he came back a couple of times, so I guess I remembered wrong.
I guess maybe they were talking about crossing the line of making a premeditated choice to kill someone, as opposed to a heat-of-battle, last-resort thing. But didn't Barry already make that choice with Reverse Flash at some point, even though he didn't go through with it?